rs6459959

Variant names:

• chr7-155905457-C-G
• rs6459959

Your query was ambiguous. Multiple possible variants found:

• chr7-155905457-C-G
• chr7-155905457-C-T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.619 in 152,148 control chromosomes in the GnomAD database, including 29,421 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.62 (29421 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.64
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.634 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.619 AC: 94112 AN: 152030 Hom.: 29414 Cov.: 33

Gnomad AFR AF: 0.608

Gnomad AMI AF: 0.556

Gnomad AMR AF: 0.519

Gnomad ASJ AF: 0.761

Gnomad EAS AF: 0.632

Gnomad SAS AF: 0.614

Gnomad FIN AF: 0.625

Gnomad MID AF: 0.744

Gnomad NFE AF: 0.640

Gnomad OTH AF: 0.622

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.619 AC: 94147 AN: 152148 Hom.: 29421 Cov.: 33 AF XY: 0.618 AC XY: 45939 AN XY: 74376

African (AFR) AF: 0.608 AC: 25234 AN: 41500

American (AMR) AF: 0.518 AC: 7919 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.761 AC: 2641 AN: 3470

East Asian (EAS) AF: 0.632 AC: 3267 AN: 5170

South Asian (SAS) AF: 0.612 AC: 2946 AN: 4816

European-Finnish (FIN) AF: 0.625 AC: 6614 AN: 10574

Middle Eastern (MID) AF: 0.728 AC: 214 AN: 294

European-Non Finnish (NFE) AF: 0.639 AC: 43494 AN: 68014

Other (OTH) AF: 0.620 AC: 1311 AN: 2114

Alfa AF: 0.478 Hom.: 1265

Bravo AF: 0.611

Asia WGS AF: 0.600 AC: 2084 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	1.7
DANN	Benign	0.45
PhyloP100		-1.6

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs6459959; hg19: chr7-155698151;